Abstract
Phylogenetic tree reconciliation is a widely used approach for analyzing the inconsistencies between the evolutionary histories of genes, and the species through which they have evolved. An important aspect of tree reconciliation are the cost functions involved that are the minimum number of evolutionary events explaining such inconsistencies. Mean values for these functions are fundamental when analyzing tree reconciliations. Here we describe mean value formulas when a history of genes is fixed for the cost functions for the events gene duplication, gene loss and gene duplication-loss, under the uniform model of species trees. We show that these formulas can be efficiently computed, and finally analyze the mean values using empirical and simulated data.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akerborg, O., Sennblad, B., Arvestad, L., Lagergren, J.: Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Natl. Acad. Sci. U.S.A. 106(14), 5714–5719 (2009)
Altenhoff, A.M., Dessimoz, C.: Inferring orthology and paralogy. Methods Mol. Biol. 855, 259–279 (2012)
Bininda-Emonds, O.R. (ed.): Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Computational Biology, vol. 4. Springer, Netherlands (2004)
Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347(1–2), 36–53 (2005)
David, L.A., Alm, E.J.: Rapid evolutionary innovation during an Archaean genetic expansion. Nature 469(7328), 93–96 (2011)
Eulenstein, O., Huzurbazar, S., Liberles, D.: Reconciling phylogenetic trees. In: Evolution After Gene Duplication, pp. 185–206. Wiley (2010)
Eulenstein, O.: Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. Ph.D. thesis, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany (1998)
Furnas, G.W.: The generation of random, binary unordered trees. J. Classif. 1(1), 187–233 (1984)
Goodman, M., et al.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28(2), 132–163 (1979)
Górecki, P., Eulenstein, O.: Bijective diameters of gene tree parsimony costs (2017, submitted)
Górecki, P., Eulenstein, O.: Deep coalescence reconciliation with unrooted gene trees: linear time algorithms. In: Gudmundsson, J., Mestre, J., Viglas, T. (eds.) COCOON 2012. LNCS, vol. 7434, pp. 531–542. Springer, Heidelberg (2012). doi:10.1007/978-3-642-32241-9_45
Górecki, P., Eulenstein, O.: Maximizing deep coalescence cost. IEEE-ACM Trans. Comput. Biol. Bioinform. 11(1), 231–242 (2014)
Górecki, P., Eulenstein, O.: Gene tree diameter for deep coalescence. IEEE-ACM Trans. Comput. Biol. Bioinform. 12(1), 155–165 (2015)
Górecki, P., Paszek, J., Eulenstein, O.: Unconstrained gene tree diameters for deep coalescence. In: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2014, pp. 114–121. ACM, New York (2014)
Górecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theor. Comput. Sci. 359(1–3), 378–399 (2006)
Górecki, P., Eulenstein, O., Tiuryn, J.: Unrooted tree reconciliation: a unified approach. IEEE-ACM Trans. Comput. Biol. Bioinform. 10(2), 522–536 (2013)
Górecki, P., Paszek, J., Mykowiecka, A.: Mean values of gene duplication and loss cost functions. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds.) ISBRA 2016. LNCS, vol. 9683, pp. 189–199. Springer, Cham (2016). doi:10.1007/978-3-319-38782-6_16
Harding, E.F.: The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab. 3(1), 44–77 (1971)
Ihara, K., Umemura, T., Katagiri, I., Kitajima-Ihara, T., Sugiyama, Y., Kimura, Y., Mukohata, Y.: Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J. Mol. Biol. 285(1), 163–174 (1999)
Kamneva, O.K., Knight, S.J., Liberles, D.A., Ward, N.L.: Analysis of genome content evolution in PVC bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol. Evol. 4(12), 1375–1390 (2012)
Kamneva, O.K., Ward, N.L.: Reconciliation approaches to determining HGT, duplications, and losses in gene trees. In: Goodfellow, M., Chun, J., Sutcliffe, I.C. (eds.) New Approaches to Prokaryotic Systematics, Methods in Microbiology, chap. 9, vol. 41, pp. 183–199. Academic Press (2014)
Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46, 523–536 (1997)
Maddison, W.P., Knowles, L.L.: Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55(1), 21–30 (2006)
McKenzie, A., Steel, M.: Distributions of cherries for two models of trees. Math. Biosci. 164(1), 81–92 (2000)
Page, R.: From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7(2), 231–240 (1997)
Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43(1), 58–77 (1994)
Ruan, J., et al.: TreeFam: 2008 update. Nucleic Acids Res. 36, D735–D740 (2008)
Steel, M.A., Penny, D.: Distributions of tree comparison metrics – some new results. Syst. Biol. 42(2), 126–141 (1993)
Than, C.V., Rosenberg, N.A.: Mean deep coalescence cost under exchangeable probability distributions. Discret. Appl. Math. 174, 11–26 (2014)
Wehe, A., Burleigh, J.G.: Scaling the gene duplication problem towards the tree of life: accelerating the rSPR heuristic search (2010)
Zhang, L.: From gene trees to species trees II: species tree inference by minimizing deep coalescence events. IEEE-ACM Trans. Comput. Biol. Bioinform. 8, 1685–1691 (2011)
Acknowledgements
This material is based upon work supported by the grants of the National Science Foundation under Grant No. 1617626 and the NCN #2015/19/B/ST6/00726.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Górecki, P., Markin, A., Mykowiecka, A., Paszek, J., Eulenstein, O. (2017). Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees. In: Cai, Z., Daescu, O., Li, M. (eds) Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science(), vol 10330. Springer, Cham. https://doi.org/10.1007/978-3-319-59575-7_21
Download citation
DOI: https://doi.org/10.1007/978-3-319-59575-7_21
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-59574-0
Online ISBN: 978-3-319-59575-7
eBook Packages: Computer ScienceComputer Science (R0)